[English] 日本語
Yorodumi
- EMDB-25037: Cryo-EM 3D map of the human Exostosin-1 and Exostosin-2 heterodim... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25037
TitleCryo-EM 3D map of the human Exostosin-1 and Exostosin-2 heterodimer in complex with a 7-sugar oligosaccharide acceptor analog
Map data
Sample
  • Complex: human EXT1/2
    • Protein or peptide: Exostosin-1
    • Protein or peptide: Exostosin-2
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MANGANESE (II) ION
Function / homology
Function and homology information


glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase / hypersensitivity / heart field specification / lymphocyte adhesion to endothelial cell of high endothelial venule / heparan sulfate N-acetylglucosaminyltransferase activity / glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity / smoothened signaling pathway involved in lung development / developmental growth involved in morphogenesis ...glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase / hypersensitivity / heart field specification / lymphocyte adhesion to endothelial cell of high endothelial venule / heparan sulfate N-acetylglucosaminyltransferase activity / glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity / smoothened signaling pathway involved in lung development / developmental growth involved in morphogenesis / sweat gland development / perichondral bone morphogenesis / mesenchymal cell differentiation involved in bone development / response to leukemia inhibitory factor / chondroitin sulfate metabolic process / UDP-N-acetylglucosamine transferase complex / response to heparin / chondrocyte hypertrophy / embryonic skeletal joint development / hematopoietic stem cell migration to bone marrow / : / heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process / fluid transport / glucuronosyltransferase activity / limb joint morphogenesis / tight junction organization / heparin biosynthetic process / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / stomach development / sebaceous gland development / glomerular basement membrane development / dendrite self-avoidance / heparan sulfate proteoglycan biosynthetic process / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / lymphocyte migration into lymphoid organs / chondrocyte proliferation / sulfation / hematopoietic stem cell homeostasis / podocyte differentiation / glandular epithelial cell differentiation / dendritic cell migration / endochondral bone morphogenesis / polysaccharide biosynthetic process / sodium ion homeostasis / endochondral bone growth / acetylglucosaminyltransferase activity / response to light intensity / basement membrane organization / cartilage development involved in endochondral bone morphogenesis / cranial skeletal system development / vocalization behavior / stem cell division / endoderm development / multicellular organismal-level water homeostasis / leukocyte tethering or rolling / vacuole organization / olfactory bulb development / endochondral ossification / fear response / optic nerve development / protein N-linked glycosylation / cellular response to fibroblast growth factor stimulus / neural crest cell differentiation / collagen fibril organization / ossification involved in bone maturation / motor behavior / cell adhesion mediated by integrin / epithelial tube branching involved in lung morphogenesis / hair follicle morphogenesis / heart contraction / glycosyltransferase activity / protein glycosylation / social behavior / mesoderm development / mesoderm formation / catalytic complex / antigen processing and presentation / canonical Wnt signaling pathway / gastrulation / hematopoietic stem cell differentiation / fibroblast growth factor receptor signaling pathway / blood vessel remodeling / cell fate commitment / chondrocyte differentiation / BMP signaling pathway / bone resorption / ossification / synaptic transmission, glutamatergic / axon guidance / protein catabolic process / multicellular organism growth / wound healing / cellular response to virus / regulation of blood pressure / vasodilation / gene expression / protein-containing complex assembly / protein heterodimerization activity
Similarity search - Function
Exostosin-like / Exostosin, GT47 domain / Exostosin family / Glycosyl transferase 64 domain / Glycosyl transferase family 64 domain / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Exostosin-1 / Exostosin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLi H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA231466 United States
CitationJournal: Nat Chem Biol / Year: 2023
Title: Structural basis for heparan sulfate co-polymerase action by the EXT1-2 complex.
Authors: Hua Li / Digantkumar Chapla / Robert A Amos / Annapoorani Ramiah / Kelley W Moremen / Huilin Li /
Abstract: Heparan sulfate (HS) proteoglycans are extended (-GlcAβ1,4GlcNAcα1,4-) co-polymers containing decorations of sulfation and epimerization that are linked to cell surface and extracellular matrix ...Heparan sulfate (HS) proteoglycans are extended (-GlcAβ1,4GlcNAcα1,4-) co-polymers containing decorations of sulfation and epimerization that are linked to cell surface and extracellular matrix proteins. In mammals, HS repeat units are extended by an obligate heterocomplex of two exostosin family members, EXT1 and EXT2, where each protein monomer contains distinct GT47 (GT-B fold) and GT64 (GT-A fold) glycosyltransferase domains. In this study, we generated human EXT1-EXT2 (EXT1-2) as a functional heterocomplex and determined its structure in the presence of bound donor and acceptor substrates. Structural data and enzyme activity of catalytic site mutants demonstrate that only two of the four glycosyltransferase domains are major contributors to co-polymer syntheses: the EXT1 GT-B fold β1,4GlcA transferase domain and the EXT2 GT-A fold α1,4GlcNAc transferase domain. The two catalytic sites are over 90 Å apart, indicating that HS is synthesized by a dissociative process that involves a single catalytic site on each monomer.
History
DepositionSep 28, 2021-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25037.png

Downloads & links

-
Map

FileDownload / File: emd_25037.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.968 Å		0.83 Å/pix.
x 256 pix.
= 211.968 Å		0.83 Å/pix.
x 256 pix.
= 211.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0131
Minimum - Maximum-0.0017577211 - 2.2084262
Average (Standard dev.)0.0024533528 (±0.036012698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.968 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_25037_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_25037_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_25037_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_25037_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human EXT1/2

EntireName: human EXT1/2
Components
  • Complex: human EXT1/2
    • Protein or peptide: Exostosin-1
    • Protein or peptide: Exostosin-2
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MANGANESE (II) ION

-
Supramolecule #1: human EXT1/2

SupramoleculeName: human EXT1/2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Exostosin-1

MacromoleculeName: Exostosin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.404023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GFRASRSHSR REEHSGRNGL HHPSPDHFWP RFPDALRPFV PWDQLENEDS SVHISPRQKR DANSSIYKGK KCRMESCFDF TLCKKNGFK VYVYPQQKGE KIAESYQNIL AAIEGSRFYT SDPSQACLFV LSLDTLDRDQ LSPQYVHNLR SKVQSLHLWN N GRNHLIFN ...String:
GFRASRSHSR REEHSGRNGL HHPSPDHFWP RFPDALRPFV PWDQLENEDS SVHISPRQKR DANSSIYKGK KCRMESCFDF TLCKKNGFK VYVYPQQKGE KIAESYQNIL AAIEGSRFYT SDPSQACLFV LSLDTLDRDQ LSPQYVHNLR SKVQSLHLWN N GRNHLIFN LYSGTWPDYT EDVGFDIGQA MLAKASISTE NFRPNFDVSI PLFSKDHPRT GGERGFLKFN TIPPLRKYML VF KGKRYLT GIGSDTRNAL YHVHNGEDVV LLTTCKHGKD WQKHKDSRCD RDNTEYEKYD YREMLHNATF CLVPRGRRLG SFR FLEALQ AACVPVMLSN GWELPFSEVI NWNQAAVIGD ERLLLQIPST IRSIHQDKIL ALRQQTQFLW EAYFSSVEKI VLTT LEIIQ DRIFKHISRN SLIWNKHPGG LFVLPQYSSY LGDFPYYYAN LGLKPPSKFT AVIHAVTPLV SQSQPVLKLL VAAAK SQYC AQIIVLWNCD KPLPAKHRWP ATAVPVVVIE GESKVMSSRF LPYDNIITDA VLSLDEDTVL STTEVDFAFT VWQSFP ERI VGYPARSHFW DNSKERWGYT SKWTNDYSMV LTGAAIYHKY YHYLYSHYLP ASLKNMVDQL ANCEDILMNF LVSAVTK LP PIKVTQKKQY KETMMGQTSR ASRWADPDHF AQRQSCMNTF ASWFGYMPLI HSQMRLDPVL FKDQVSILRK KYRDIERL

-
Macromolecule #2: Exostosin-2

MacromoleculeName: Exostosin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.238031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GWPHSIESSN DWNVEKRSIR DVPVVRLPAD SPIPERGDLS CRMHTCFDVY RCGFNPKNKI KVYIYALKKY VDDFGVSVSN TISREYNEL LMAISDSDYY TDDINRACLF VPSIDVLNQN TLRIKETAQA MAQLSRWDRG TNHLLFNMLP GGPPDYNTAL D VPRDRALL ...String:
GWPHSIESSN DWNVEKRSIR DVPVVRLPAD SPIPERGDLS CRMHTCFDVY RCGFNPKNKI KVYIYALKKY VDDFGVSVSN TISREYNEL LMAISDSDYY TDDINRACLF VPSIDVLNQN TLRIKETAQA MAQLSRWDRG TNHLLFNMLP GGPPDYNTAL D VPRDRALL AGGGFSTWTY RQGYDVSIPV YSPLSAEVDL PEKGPGPRQY FLLSSQVGLH PEYREDLEAL QVKHGESVLV LD KCTNLSE GVLSVRKRCH KHQVFDYPQV LQEATFCVVL RGARLGQAVL SDVLQAGCVP VVIADSYILP FSEVLDWKRA SVV VPEEKM SDVYSILQSI PQRQIEEMQR QARWFWEAYF QSIKAIALAT LQIINDRIYP YAAISYEEWN DPPAVKWGSV SNPL FLPLI PPQSQGFTAI VLTYDRVESL FRVITEVSKV PSLSKLLVVW NNQNKNPPED SLWPKIRVPL KVVRTAENKL SNRFF PYDE IETEAVLAID DDIIMLTSDE LQFGYEVWRE FPDRLVGYPG RLHLWDHEMN KWKYESEWTN EVSMVLTGAA FYHKYF NYL YTYKMPGDIK NWVDAHMNCE DIAMNFLVAN VTGKAVIKVT PRKKFKCPEC TAIDGLSLDQ THMVERSECI NKFASVF GT MPLKVVEHRA DPVLYKDDFP EKLKSFPNIG SL

-
Macromolecule #5: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM / Uridine diphosphate

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Macromolecule #7: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMHEPESHEPES
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 299 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 193.0 K / Max: 193.0 K
Alignment procedureComa free - Residual tilt: 0.05 mrad
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 5108 / #0 - Average exposure time: 1.5 sec. / #0 - Average electron dose: 68.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Digitization - Dimensions - Width: 5760 pixel / #1 - Digitization - Dimensions - Height: 4092 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 7609 / #1 - Average exposure time: 1.5 sec. / #1 - Average electron dose: 72.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 11177472
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 321316
Image recording ID1
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7sck:
Cryo-EM structure of the human Exostosin-1 and Exostosin-2 heterodimer in complex with a 7-sugar oligosaccharide acceptor analog

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more